A coupled three-dimensional physical model and a nitrogen-based nutrient, phytoplankton, zooplankton, and detritus (NPZD) ecosystem model were applied to simulate the summer coastal upwelling system over the continental shelf of northern South China Sea (NSCS) and its impact on hydrographic conditions and ecosystem. The simulated results were comprehensively validated against field and satellite measurements. The model results show that the near shore ecosystem of NSCS has significant responses to the summer coastal upwelling system. The Shantou Coast to the Nanri Islands of Fujian province (YD) and the east of the Leizhou Peninsula (QD) are two main regions affected by NSCS summer coast upwelling. During summer, these two coastal areas are characterized by nearshore cold and high salinity upwelling current. Further, the summer coastal upwelling serves as a perfect nutrient pump, which lifts up and advects nutrient-rich current from deep to surface, from inner shelf to about 30 km outer shelf. This nutrient source reaches its maximum in the middle of July and then begins to decrease. However, the maximum phytoplankton and chlorophyll a do not coincide with the maximum nutrients and delay for about 10 days. Because of the intensive seasonal thermocline and the complicated current transporting through Qiongzhou strait, the ecological responding of QD is less pronounced than YD. This study has a better understanding of the physically modulated ecological responses to the NSCS summer coastal upwelling system.